[Chimera-users] Batch mode for Chimera

James Starlight jmsstarlight at gmail.com
Mon Sep 4 01:09:29 PDT 2017


Hi Greg,

I am using Ubuntu with Nvidia driver.

I have updated all those packages and copy files to chimera_batch lib
dir but it was the same effect.

then I found that the problem was hidden in my batch script!
"preset apply pub 2" produced that crash !
but if I change it to "preset app int all" everything is fine.

P.S. as I found in the resulted images on the default the protein is
aligned along its Z vector. Is it possible to turn it via some command
to display in-front or in the pseudo-isometrical projection?

Thanks!!

Gleb

2017-09-04 10:08 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> Hi Greg,
>
> I am using Ubuntu with Nvidia driver.
>
> I have updated all those packages and copy files to chimera_batch lib
> dir but it was the same effect.
>
> then I found that the problem was hidden in my batch script!
> "preset apply pub 2" produced that crash !
> but if I change it to "preset app int all" everything is fine.
>
> P.S. as I found in the resulted images on the default the protein is
> aligned along its Z vector. Is it possible to turn it via some command
> to display in-front or in the pseudo-isometrical projection?
>
> Thanks!!
>
> Gleb
>
> 2017-09-03 2:58 GMT+02:00 Greg Couch <gregc at cgl.ucsf.edu>:
>> My guess is it is a graphics driver problem.
>>
>> We haven't updated the software OpenGL driver that is bundled with the
>> headless Chimera in ages (Mesa 7.6.1), but we have updated Chimera's use of
>> OpenGL.  Chances are that your Linux server has newer version.  So assuming
>> you don't have a graphics driver installed, you should try moving aside the
>> libGL.so* and libOSMesa.so* files in your
>> /home/gleb/.local/UCSF-Chimera64-batch/lib directory so chimera will use the
>> system versions.  You might need to install those libraries on your system.
>> On CentOS/RHEL, they are the mesa-libOSMesa and mesa-libGL packages.  On
>> Debian/Ubuntu, they are the libosmesa6 and libgl1-mesa-dev packages.
>>
>> If you have an AMD/NVIDIA graphics driver installed, then you will want to
>> copy the Mesa versions of libGL.so and libOSMesa.so to your
>> /home/gleb/.local/UCSF-Chimera64-batch/lib directory.   On CentOS/RHEL, the
>> AMD/NVIDIA installers should have moved  the Mesa versions aside somewhere,
>> so they could be restored with the driver is uninstalled -- it will take
>> some detective work to find them.  On Ubuntu, the libGL.so* files are in
>> /usr/lib/x86_64-linux-gnu/mesa/.
>>
>>     HTH,
>>
>>     Greg
>>
>>
>>
>> On 9/1/2017 1:23 AM, James Starlight wrote:
>>>
>>> now the errors of the execution of the script using headless chimera:
>>>
>>> Opening rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb...
>>> The following problems occurred while reading PDB file for
>>> rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb
>>> warning:  Ignored bad PDB record found on line 2
>>>
>>> Opened rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb containing 1 model, 903
>>> atoms, and 301 residues
>>> Rendering high resolution image...
>>> ./run.sh: line 113: 14479 Segmentation fault      (core dumped)
>>> chimera_batch $pdb "${temp}"/script_${name}.cmd
>>>
>>>
>>> the same with a pow-ray render
>>>
>>> Opened rmsf_visu_AT1_wat_Na.3rep.step7_1.pdb containing 1 model, 903
>>> atoms, and 301 residues
>>> Generating POV-Ray data file
>>> Exporting POV-Ray data to
>>>
>>> /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/rmsf_AT1_wat_Na.3rep.pov
>>> Ignoring CHIMERA environment variable
>>> Parse error at line 1:
>>>   no element found
>>>
>>>
>>> here is my script:
>>>
>>> preset apply publication 2
>>> rangecolor bfactor 2 blue 30 red 50 yellow
>>> copy file
>>> /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/AT1_wat_apo.3rep.png
>>> png width 800 height 600
>>>
>>>
>>> I have made the same images in chimera GUI and it worked very well.
>>>
>>> Is it possible to run same script using in chimera-gui but from batch
>>> mode?
>>>
>>> 2017-08-31 22:04 GMT+02:00 Greg Couch <gregc at cgl.ucsf.edu>:
>>>>
>>>> You must have the given the "key" argument to the rangecolor command.
>>>> That
>>>> option tries to display the Color Key tool which want you to use the
>>>> mouse
>>>> to position the color key in the graphics window.  That is not possible
>>>> in
>>>> batch mode.  You'll need to add the color key afterwards with an image
>>>> editor if you need it.
>>>>
>>>>      HTH,
>>>>
>>>>      Greg
>>>>
>>>>
>>>>
>>>> On 08/31/2017 01:00 AM, James Starlight wrote:
>>>>>
>>>>> Thanks Eric!
>>>>>
>>>>> Everything works fine with the exception of the copy command. On the
>>>>> rendering stage I have:
>>>>>
>>>>>
>>>>> Opened AT1_dry_apo.1rep.step7_1.pdb containing 1 model, 57791 atoms,
>>>>> and 12661 residues
>>>>> Traceback (most recent call last):
>>>>>     File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimeraInit.py",
>>>>> line 683, in init
>>>>>       chimera.openModels.open(a, prefixableType=1)
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/__init__.py",
>>>>> line 1951, in open
>>>>>       models = func(filename, *args, **kw)
>>>>>     File
>>>>>
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/ChimeraExtension.py",
>>>>> line 31, in func
>>>>>       processCommandFile(fileName)
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>>>>> line 108, in processCommandFile
>>>>>       _processFile(f, emulateRead, filename)
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>>>>> line 143, in _processFile
>>>>>       if makeCommand(line):
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>>>>> line 69, in makeCommand
>>>>>       f(c, args)
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py",
>>>>> line 1786, in doRangeColor
>>>>>       showKey=key)
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/__init__.py",
>>>>> line 2526, in rangeColor
>>>>>       from Ilabel.gui import IlabelDialog
>>>>>     File "/home/gleb/.local/UCSF-Chimera64-batch/share/Ilabel/gui.py",
>>>>> line 13, in <module>
>>>>>       from chimera import tkgui, chimage, CLOSE_SESSION
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py",
>>>>> line 74, in <module>
>>>>>       import Togl
>>>>> ImportError: No module named Togl
>>>>>
>>>>> Error while processing
>>>>>
>>>>>
>>>>> /home/gleb/Desktop/Scripts/MegaAnalysis/temp/script_AT1_dry_apo.1rep.step7_1.pdb.cmd:
>>>>> ImportError: No module named Togl
>>>>>
>>>>>     File
>>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py",
>>>>> line 74, in <module>
>>>>>       import Togl
>>>>>
>>>>> See reply log for Python traceback.
>>>>>
>>>>> I have found that it is due to some conflict in PYTHONPATH from my
>>>>> bash since I am running Chimera directly from BASH. The people also
>>>>> wrote that Its related to setting transparency-  which was not a case
>>>>> there - I did not set in my script. Anyway how to fix it?
>>>>>
>>>>> Thanks you!
>>>>>
>>>>> James
>>>>>
>>>>> 2017-08-30 22:54 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>>>>>
>>>>>> Hi James,
>>>>>> First, if you want to save images without showing the Chimera GUI then
>>>>>> you
>>>>>> have to use the “headless” version of Chimera, available on the
>>>>>> download
>>>>>> page.  To do the other things you want, just put the equivalent
>>>>>> commands
>>>>>> in
>>>>>> a file that ends in “.cmd” and just add that file to your invocation of
>>>>>> Chimera, e.g.:
>>>>>>
>>>>>> chimera $pdb script.cmd
>>>>>>
>>>>>> The easiest way to handle the image file name is probably to used a
>>>>>> fixed
>>>>>> name in the Chimera “copy” command, and then in your bash script move
>>>>>> that
>>>>>> file to the final name you want.  Also, "preset” is the command to
>>>>>> apply
>>>>>> presets — “help preset” in Chimera for more info.
>>>>>>
>>>>>> Hope this helps.
>>>>>>
>>>>>> —Eric
>>>>>>
>>>>>>
>>>>>> Eric Pettersen
>>>>>> UCSF Computer Graphics Lab
>>>>>>
>>>>>>
>>>>>> On Aug 30, 2017, at 8:40 AM, James Starlight <jmsstarlight at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Dear Chimera Users!
>>>>>>
>>>>>> My simple bash script loops the folder with the pdbs and open it in
>>>>>> Chimera
>>>>>>
>>>>>> for pdb in ${output}/xtc_proc/*.pdb ; do
>>>>>> name=$(basename "$pdb")
>>>>>> echo "I am sending ${name} to Chimera!"
>>>>>> chimera $pdb
>>>>>> done
>>>>>>
>>>>>> My question - can I use with chimera some batch file which will
>>>>>> apply the following commands to each of the loaded pdbs without
>>>>>> opening of Chimera GUI:
>>>>>>
>>>>>> 1- Apply "publications-2" preset
>>>>>>
>>>>>> 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb
>>>>>> according to b-factor provided in the pdb file
>>>>>>
>>>>>> 3- make a screen-shot of the colored cartoon figure in the selected
>>>>>> output folder.
>>>>>>
>>>>>>
>>>>>> I thanks so much for the example of batch file and the syntax accepted
>>>>>> by chimera from the linux shell.
>>>>>>
>>>>>> James
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>>>>>>
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